Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1JW8CH9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1JW8CH9
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 79 arm-level events and 9 clinical features across 498 patients, 24 significant findings detected with Q value < 0.25.

  • 3q gain cnv correlated to 'PATHOLOGY.T.STAGE'.

  • 5p gain cnv correlated to 'AGE'.

  • 20p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 20q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 4p loss cnv correlated to 'Time to Death' and 'PATHOLOGY.T.STAGE'.

  • 4q loss cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • 5p loss cnv correlated to 'PATHOLOGY.T.STAGE'.

  • 9p loss cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • 9q loss cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • 13q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 14q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 18p loss cnv correlated to 'PATHOLOGY.T.STAGE'.

  • 19p loss cnv correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 24 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBERPACKYEARSSMOKED
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test t-test
4q loss 65 (13%) 433 2.85e-06
(0.00172) 		0.9
(1.00) 		1.63e-05
(0.00974) 		6.63e-06
(0.00397) 		0.466
(1.00) 		0.00848
(1.00) 		0.333
(1.00) 		0.193
(1.00)
9p loss 144 (29%) 354 1.17e-05
(0.00702) 		0.0691
(1.00) 		4.58e-06
(0.00276) 		5.51e-05
(0.0327) 		0.101
(1.00) 		0.00175
(0.988) 		0.000873
(0.501) 		0.576
(1.00)
9q loss 145 (29%) 353 0.000239
(0.14) 		0.0498
(1.00) 		1.66e-06
(0.001) 		5.19e-06
(0.00312) 		0.171
(1.00) 		0.00465
(1.00) 		0.00063
(0.362) 		0.487
(1.00)
20p gain 110 (22%) 388 0.187
(1.00) 		0.194
(1.00) 		8.79e-05
(0.052) 		5.35e-06
(0.00321) 		0.547
(1.00) 		0.0242
(1.00) 		0.00141
(0.8) 		0.373
(1.00)
20q gain 113 (23%) 385 0.143
(1.00) 		0.0614
(1.00) 		6.04e-05
(0.0358) 		1.9e-05
(0.0113) 		0.239
(1.00) 		0.0332
(1.00) 		0.00683
(1.00) 		0.373
(1.00)
4p loss 71 (14%) 427 1.68e-05
(0.00999) 		0.971
(1.00) 		0.000452
(0.262) 		0.000285
(0.167) 		0.727
(1.00) 		0.0569
(1.00) 		0.894
(1.00) 		0.13
(1.00)
13q loss 69 (14%) 429 0.00106
(0.606) 		0.558
(1.00) 		0.000211
(0.124) 		3.14e-06
(0.00189) 		0.323
(1.00) 		0.105
(1.00) 		0.34
(1.00) 		0.669
(1.00)
14q loss 209 (42%) 289 0.00107
(0.611) 		0.165
(1.00) 		4.38e-05
(0.026) 		0.000322
(0.188) 		0.00248
(1.00) 		0.00173
(0.978) 		0.0707
(1.00) 		0.0872
(1.00)
3q gain 59 (12%) 439 0.394
(1.00) 		0.625
(1.00) 		0.00233
(1.00) 		0.000339
(0.198) 		0.00753
(1.00) 		0.018
(1.00) 		1
(1.00) 		0.193
(1.00)
5p gain 186 (37%) 312 0.0576
(1.00) 		0.000199
(0.117) 		0.161
(1.00) 		0.298
(1.00) 		0.62
(1.00) 		0.696
(1.00) 		0.0254
(1.00) 		0.572
(1.00)
5p loss 7 (1%) 491 0.0187
(1.00) 		0.291
(1.00) 		0.00189
(1.00) 		0.000195
(0.115) 		1
(1.00) 		0.12
(1.00) 		0.243
(1.00)
18p loss 91 (18%) 407 0.00286
(1.00) 		0.123
(1.00) 		0.000573
(0.331) 		0.000359
(0.209) 		1
(1.00) 		0.172
(1.00) 		0.182
(1.00) 		0.494
(1.00)
19p loss 11 (2%) 487 0.00017
(0.1) 		0.0391
(1.00) 		0.0329
(1.00) 		0.000893
(0.512) 		1
(1.00) 		0.431
(1.00) 		0.755
(1.00)
1p gain 22 (4%) 476 0.00271
(1.00) 		0.303
(1.00) 		0.324
(1.00) 		0.328
(1.00) 		0.214
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.482
(1.00)
1q gain 50 (10%) 448 0.0833
(1.00) 		0.0691
(1.00) 		0.132
(1.00) 		0.169
(1.00) 		0.427
(1.00) 		0.769
(1.00) 		0.755
(1.00) 		0.499
(1.00)
2p gain 75 (15%) 423 0.813
(1.00) 		0.148
(1.00) 		0.188
(1.00) 		0.463
(1.00) 		1
(1.00) 		0.323
(1.00) 		0.794
(1.00) 		0.491
(1.00)
2q gain 76 (15%) 422 0.663
(1.00) 		0.2
(1.00) 		0.327
(1.00) 		0.715
(1.00) 		1
(1.00) 		0.266
(1.00) 		0.361
(1.00) 		0.387
(1.00)
3p gain 20 (4%) 478 0.0783
(1.00) 		0.852
(1.00) 		0.103
(1.00) 		0.177
(1.00) 		0.0587
(1.00) 		0.211
(1.00) 		0.344
(1.00) 		0.328
(1.00)
4p gain 13 (3%) 485 0.0984
(1.00) 		0.865
(1.00) 		0.468
(1.00) 		0.209
(1.00) 		0.5
(1.00) 		1
(1.00) 		0.557
(1.00)
4q gain 13 (3%) 485 0.296
(1.00) 		0.865
(1.00) 		0.575
(1.00) 		0.755
(1.00) 		0.459
(1.00) 		0.725
(1.00) 		1
(1.00)
5q gain 199 (40%) 299 0.0609
(1.00) 		0.000608
(0.35) 		0.415
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.0348
(1.00) 		0.572
(1.00)
6p gain 11 (2%) 487 0.744
(1.00) 		0.775
(1.00) 		0.384
(1.00) 		0.274
(1.00) 		1
(1.00) 		0.707
(1.00) 		0.344
(1.00)
6q gain 9 (2%) 489 0.536
(1.00) 		0.321
(1.00) 		0.268
(1.00) 		0.298
(1.00) 		1
(1.00) 		1
(1.00) 		0.172
(1.00)
7p gain 166 (33%) 332 1
(1.00) 		0.443
(1.00) 		0.0857
(1.00) 		0.137
(1.00) 		0.449
(1.00) 		0.0487
(1.00) 		0.00375
(1.00) 		0.711
(1.00)
7q gain 167 (34%) 331 0.511
(1.00) 		0.498
(1.00) 		0.019
(1.00) 		0.0663
(1.00) 		0.443
(1.00) 		0.00492
(1.00) 		0.00968
(1.00) 		0.528
(1.00)
8p gain 29 (6%) 469 0.543
(1.00) 		0.249
(1.00) 		0.00562
(1.00) 		0.00419
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.841
(1.00) 		0.757
(1.00)
8q gain 57 (11%) 441 0.342
(1.00) 		0.0745
(1.00) 		0.0197
(1.00) 		0.00561
(1.00) 		0.427
(1.00) 		0.156
(1.00) 		0.302
(1.00) 		0.471
(1.00)
9p gain 13 (3%) 485 0.269
(1.00) 		0.563
(1.00) 		0.947
(1.00) 		0.0521
(1.00) 		1
(1.00) 		0.296
(1.00) 		0.0145
(1.00)
9q gain 12 (2%) 486 0.961
(1.00) 		0.337
(1.00) 		0.243
(1.00) 		0.00315
(1.00) 		1
(1.00) 		1
(1.00) 		0.121
(1.00)
10p gain 17 (3%) 481 0.774
(1.00) 		0.148
(1.00) 		0.356
(1.00) 		0.105
(1.00) 		0.108
(1.00) 		0.765
(1.00) 		0.798
(1.00) 		0.887
(1.00)
10q gain 12 (2%) 486 0.663
(1.00) 		0.0405
(1.00) 		0.827
(1.00) 		0.884
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.357
(1.00) 		0.81
(1.00)
11p gain 31 (6%) 467 0.997
(1.00) 		0.932
(1.00) 		0.0484
(1.00) 		0.0222
(1.00) 		1
(1.00) 		0.045
(1.00) 		0.847
(1.00) 		0.484
(1.00)
11q gain 29 (6%) 469 0.491
(1.00) 		0.999
(1.00) 		0.243
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.102
(1.00) 		1
(1.00)
12p gain 117 (23%) 381 0.00915
(1.00) 		0.0445
(1.00) 		0.00167
(0.945) 		0.00513
(1.00) 		0.258
(1.00) 		0.047
(1.00) 		0.581
(1.00) 		0.268
(1.00)
12q gain 117 (23%) 381 0.0139
(1.00) 		0.1
(1.00) 		0.00167
(0.945) 		0.00513
(1.00) 		0.404
(1.00) 		0.047
(1.00) 		0.581
(1.00) 		0.268
(1.00)
13q gain 22 (4%) 476 0.226
(1.00) 		0.338
(1.00) 		0.178
(1.00) 		0.264
(1.00) 		1
(1.00) 		0.448
(1.00) 		0.261
(1.00)
14q gain 16 (3%) 482 0.152
(1.00) 		0.566
(1.00) 		0.285
(1.00) 		0.00793
(1.00) 		1
(1.00) 		0.362
(1.00) 		1
(1.00)
15q gain 26 (5%) 472 0.271
(1.00) 		0.378
(1.00) 		0.649
(1.00) 		0.458
(1.00) 		0.214
(1.00) 		0.645
(1.00) 		0.833
(1.00) 		0.349
(1.00)
16p gain 104 (21%) 394 0.393
(1.00) 		0.246
(1.00) 		0.226
(1.00) 		0.129
(1.00) 		0.133
(1.00) 		0.547
(1.00) 		0.818
(1.00) 		0.449
(1.00)
16q gain 96 (19%) 402 0.238
(1.00) 		0.313
(1.00) 		0.23
(1.00) 		0.0823
(1.00) 		0.212
(1.00) 		0.703
(1.00) 		0.905
(1.00) 		0.31
(1.00)
17p gain 25 (5%) 473 0.91
(1.00) 		0.365
(1.00) 		0.0766
(1.00) 		0.822
(1.00) 		0.214
(1.00) 		0.0459
(1.00) 		0.833
(1.00) 		0.74
(1.00)
17q gain 31 (6%) 467 0.576
(1.00) 		0.376
(1.00) 		0.52
(1.00) 		0.732
(1.00) 		0.3
(1.00) 		0.342
(1.00) 		1
(1.00) 		0.471
(1.00)
18p gain 25 (5%) 473 0.0456
(1.00) 		0.661
(1.00) 		0.667
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.487
(1.00) 		0.0832
(1.00)
18q gain 25 (5%) 473 0.11
(1.00) 		0.517
(1.00) 		0.541
(1.00) 		0.807
(1.00) 		0.605
(1.00) 		0.487
(1.00) 		0.0832
(1.00)
19p gain 51 (10%) 447 0.978
(1.00) 		0.641
(1.00) 		0.0111
(1.00) 		0.025
(1.00) 		0.405
(1.00) 		0.0236
(1.00) 		0.28
(1.00) 		0.716
(1.00)
19q gain 57 (11%) 441 0.555
(1.00) 		0.405
(1.00) 		0.00302
(1.00) 		0.0104
(1.00) 		0.439
(1.00) 		0.0106
(1.00) 		0.302
(1.00) 		0.716
(1.00)
21q gain 48 (10%) 450 0.567
(1.00) 		0.115
(1.00) 		0.231
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.43
(1.00) 		0.297
(1.00)
22q gain 40 (8%) 458 0.482
(1.00) 		0.481
(1.00) 		0.831
(1.00) 		0.121
(1.00) 		1
(1.00) 		0.86
(1.00) 		0.388
(1.00) 		0.829
(1.00)
xq gain 29 (6%) 469 0.841
(1.00) 		0.817
(1.00) 		0.0863
(1.00) 		0.145
(1.00) 		1
(1.00) 		0.0157
(1.00) 		0.693
(1.00) 		0.328
(1.00)
1p loss 56 (11%) 442 0.565
(1.00) 		0.0822
(1.00) 		0.371
(1.00) 		0.0107
(1.00) 		0.702
(1.00) 		0.534
(1.00) 		0.233
(1.00) 		0.297
(1.00)
1q loss 36 (7%) 462 0.71
(1.00) 		0.629
(1.00) 		0.768
(1.00) 		0.0765
(1.00) 		1
(1.00) 		0.396
(1.00) 		0.717
(1.00) 		0.484
(1.00)
2p loss 14 (3%) 484 0.998
(1.00) 		0.93
(1.00) 		0.42
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.732
(1.00) 		0.779
(1.00)
2q loss 14 (3%) 484 0.984
(1.00) 		0.911
(1.00) 		0.564
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.732
(1.00) 		0.779
(1.00)
3p loss 358 (72%) 140 0.573
(1.00) 		0.727
(1.00) 		0.0166
(1.00) 		0.0324
(1.00) 		0.793
(1.00) 		0.149
(1.00) 		0.0211
(1.00) 		0.0785
(1.00)
3q loss 99 (20%) 399 0.73
(1.00) 		0.0142
(1.00) 		0.636
(1.00) 		0.275
(1.00) 		0.746
(1.00) 		0.146
(1.00) 		0.000595
(0.344) 		0.384
(1.00)
5q loss 6 (1%) 492 0.0521
(1.00) 		0.232
(1.00) 		0.00662
(1.00) 		0.000451
(0.262) 		1
(1.00) 		0.268
(1.00) 		0.423
(1.00)
6p loss 98 (20%) 400 0.392
(1.00) 		0.428
(1.00) 		0.0711
(1.00) 		0.044
(1.00) 		0.00508
(1.00) 		0.412
(1.00) 		0.002
(1.00) 		0.122
(1.00)
6q loss 123 (25%) 375 0.493
(1.00) 		0.899
(1.00) 		0.286
(1.00) 		0.192
(1.00) 		0.00122
(0.693) 		0.719
(1.00) 		0.0637
(1.00) 		0.21
(1.00)
7q loss 3 (1%) 495 0.525
(1.00) 		0.558
(1.00) 		0.127
(1.00) 		0.011
(1.00) 		0.0729
(1.00) 		1
(1.00) 		0.555
(1.00)
8p loss 134 (27%) 364 0.354
(1.00) 		0.686
(1.00) 		0.406
(1.00) 		0.329
(1.00) 		0.776
(1.00) 		0.422
(1.00) 		0.0722
(1.00) 		0.893
(1.00)
8q loss 65 (13%) 433 0.649
(1.00) 		0.958
(1.00) 		0.631
(1.00) 		0.255
(1.00) 		0.466
(1.00) 		0.815
(1.00) 		0.0174
(1.00) 		0.654
(1.00)
10p loss 65 (13%) 433 0.382
(1.00) 		0.492
(1.00) 		0.081
(1.00) 		0.00974
(1.00) 		0.14
(1.00) 		0.726
(1.00) 		0.333
(1.00) 		0.0269
(1.00)
10q loss 86 (17%) 412 0.473
(1.00) 		0.507
(1.00) 		0.0935
(1.00) 		0.00232
(1.00) 		0.322
(1.00) 		0.789
(1.00) 		0.105
(1.00) 		0.112
(1.00)
11p loss 18 (4%) 480 0.0112
(1.00) 		0.144
(1.00) 		0.476
(1.00) 		0.444
(1.00) 		0.159
(1.00) 		0.557
(1.00) 		1
(1.00) 		0.81
(1.00)
11q loss 23 (5%) 475 0.00979
(1.00) 		0.0226
(1.00) 		0.704
(1.00) 		0.627
(1.00) 		0.243
(1.00) 		0.467
(1.00) 		0.502
(1.00) 		0.887
(1.00)
12p loss 3 (1%) 495 0.324
(1.00) 		0.754
(1.00) 		0.491
(1.00) 		0.743
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 4 (1%) 494 0.964
(1.00) 		0.342
(1.00) 		0.174
(1.00) 		0.414
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
15q loss 35 (7%) 463 0.00244
(1.00) 		0.833
(1.00) 		0.00113
(0.643) 		0.000445
(0.259) 		1
(1.00) 		0.0338
(1.00) 		0.0659
(1.00) 		0.484
(1.00)
16p loss 9 (2%) 489 0.129
(1.00) 		0.843
(1.00) 		0.259
(1.00) 		0.00912
(1.00) 		0.368
(1.00) 		1
(1.00) 		1
(1.00)
16q loss 13 (3%) 485 0.214
(1.00) 		0.913
(1.00) 		0.306
(1.00) 		0.00392
(1.00) 		0.459
(1.00) 		1
(1.00) 		1
(1.00)
17p loss 44 (9%) 454 0.377
(1.00) 		0.435
(1.00) 		0.222
(1.00) 		0.184
(1.00) 		0.376
(1.00) 		0.0852
(1.00) 		0.186
(1.00) 		0.0261
(1.00)
17q loss 28 (6%) 470 0.457
(1.00) 		0.829
(1.00) 		0.361
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.311
(1.00) 		0.312
(1.00)
18q loss 93 (19%) 405 0.0113
(1.00) 		0.138
(1.00) 		0.012
(1.00) 		0.00624
(1.00) 		1
(1.00) 		0.193
(1.00) 		0.148
(1.00) 		0.569
(1.00)
19q loss 4 (1%) 494 0.00404
(1.00) 		0.829
(1.00) 		0.245
(1.00) 		0.00309
(1.00) 		1
(1.00) 		0.14
(1.00) 		1
(1.00)
20p loss 8 (2%) 490 0.824
(1.00) 		0.704
(1.00) 		0.727
(1.00) 		0.617
(1.00) 		1
(1.00) 		0.397
(1.00) 		1
(1.00)
20q loss 3 (1%) 495 0.808
(1.00) 		0.181
(1.00) 		0.244
(1.00) 		0.111
(1.00) 		0.414
(1.00) 		1
(1.00)
21q loss 53 (11%) 445 0.638
(1.00) 		0.587
(1.00) 		0.197
(1.00) 		0.00406
(1.00) 		0.0939
(1.00) 		1
(1.00) 		0.761
(1.00) 		0.505
(1.00)
22q loss 38 (8%) 460 0.0021
(1.00) 		0.267
(1.00) 		0.0203
(1.00) 		0.16
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.726
(1.00) 		0.115
(1.00)
xq loss 44 (9%) 454 0.244
(1.00) 		0.422
(1.00) 		0.66
(1.00) 		0.21
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.186
(1.00)
'3q gain' versus 'PATHOLOGY.T.STAGE'

P value = 0.000339 (Fisher's exact test), Q value = 0.2

Table S1.  Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
3Q GAIN MUTATED 17 6 32 4
3Q GAIN WILD-TYPE 228 60 144 7

Figure S1.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p gain' versus 'AGE'

P value = 0.000199 (t-test), Q value = 0.12

Table S2.  Gene #9: '5p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 497 60.5 (12.2)
5P GAIN MUTATED 186 63.2 (11.8)
5P GAIN WILD-TYPE 311 59.0 (12.1)

Figure S2.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.79e-05 (Fisher's exact test), Q value = 0.052

Table S3.  Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 239 55 125 79
20P GAIN MUTATED 33 12 39 26
20P GAIN WILD-TYPE 206 43 86 53

Figure S3.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'PATHOLOGY.T.STAGE'

P value = 5.35e-06 (Fisher's exact test), Q value = 0.0032

Table S4.  Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
20P GAIN MUTATED 34 13 57 6
20P GAIN WILD-TYPE 211 53 119 5

Figure S4.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'20q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.04e-05 (Fisher's exact test), Q value = 0.036

Table S5.  Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 239 55 125 79
20Q GAIN MUTATED 34 12 41 26
20Q GAIN WILD-TYPE 205 43 84 53

Figure S5.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20q gain' versus 'PATHOLOGY.T.STAGE'

P value = 1.9e-05 (Fisher's exact test), Q value = 0.011

Table S6.  Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
20Q GAIN MUTATED 36 13 59 5
20Q GAIN WILD-TYPE 209 53 117 6

Figure S6.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4p loss' versus 'Time to Death'

P value = 1.68e-05 (logrank test), Q value = 0.01

Table S7.  Gene #47: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 166 0.1 - 120.6 (37.1)
4P LOSS MUTATED 71 38 0.5 - 90.3 (31.1)
4P LOSS WILD-TYPE 426 128 0.1 - 120.6 (37.2)

Figure S7.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000285 (Fisher's exact test), Q value = 0.17

Table S8.  Gene #47: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
4P LOSS MUTATED 21 8 38 4
4P LOSS WILD-TYPE 224 58 138 7

Figure S8.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4q loss' versus 'Time to Death'

P value = 2.85e-06 (logrank test), Q value = 0.0017

Table S9.  Gene #48: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 166 0.1 - 120.6 (37.1)
4Q LOSS MUTATED 65 36 1.2 - 90.3 (25.7)
4Q LOSS WILD-TYPE 432 130 0.1 - 120.6 (37.3)

Figure S9.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.63e-05 (Fisher's exact test), Q value = 0.0097

Table S10.  Gene #48: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 239 55 125 79
4Q LOSS MUTATED 15 6 24 20
4Q LOSS WILD-TYPE 224 49 101 59

Figure S10.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4q loss' versus 'PATHOLOGY.T.STAGE'

P value = 6.63e-06 (Fisher's exact test), Q value = 0.004

Table S11.  Gene #48: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
4Q LOSS MUTATED 16 8 36 5
4Q LOSS WILD-TYPE 229 58 140 6

Figure S11.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000195 (Fisher's exact test), Q value = 0.11

Table S12.  Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
5P LOSS MUTATED 0 3 2 2
5P LOSS WILD-TYPE 245 63 174 9

Figure S12.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9p loss' versus 'Time to Death'

P value = 1.17e-05 (logrank test), Q value = 0.007

Table S13.  Gene #56: '9p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 166 0.1 - 120.6 (37.1)
9P LOSS MUTATED 144 69 0.2 - 109.9 (34.9)
9P LOSS WILD-TYPE 353 97 0.1 - 120.6 (37.2)

Figure S13.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.58e-06 (Fisher's exact test), Q value = 0.0028

Table S14.  Gene #56: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 239 55 125 79
9P LOSS MUTATED 48 11 50 35
9P LOSS WILD-TYPE 191 44 75 44

Figure S14.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9p loss' versus 'PATHOLOGY.T.STAGE'

P value = 5.51e-05 (Fisher's exact test), Q value = 0.033

Table S15.  Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
9P LOSS MUTATED 52 15 72 5
9P LOSS WILD-TYPE 193 51 104 6

Figure S15.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9q loss' versus 'Time to Death'

P value = 0.000239 (logrank test), Q value = 0.14

Table S16.  Gene #57: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 166 0.1 - 120.6 (37.1)
9Q LOSS MUTATED 145 67 0.2 - 109.9 (36.5)
9Q LOSS WILD-TYPE 352 99 0.1 - 120.6 (37.2)

Figure S16.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.66e-06 (Fisher's exact test), Q value = 0.001

Table S17.  Gene #57: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 239 55 125 79
9Q LOSS MUTATED 45 14 52 34
9Q LOSS WILD-TYPE 194 41 73 45

Figure S17.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9q loss' versus 'PATHOLOGY.T.STAGE'

P value = 5.19e-06 (Fisher's exact test), Q value = 0.0031

Table S18.  Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
9Q LOSS MUTATED 48 18 75 4
9Q LOSS WILD-TYPE 197 48 101 7

Figure S18.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000211 (Fisher's exact test), Q value = 0.12

Table S19.  Gene #64: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 239 55 125 79
13Q LOSS MUTATED 23 2 25 19
13Q LOSS WILD-TYPE 216 53 100 60

Figure S19.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'13q loss' versus 'PATHOLOGY.T.STAGE'

P value = 3.14e-06 (Fisher's exact test), Q value = 0.0019

Table S20.  Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
13Q LOSS MUTATED 25 3 34 7
13Q LOSS WILD-TYPE 220 63 142 4

Figure S20.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'14q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.38e-05 (Fisher's exact test), Q value = 0.026

Table S21.  Gene #65: '14q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 239 55 125 79
14Q LOSS MUTATED 75 26 63 45
14Q LOSS WILD-TYPE 164 29 62 34

Figure S21.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'14q loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000322 (Fisher's exact test), Q value = 0.19

Table S22.  Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
14Q LOSS MUTATED 81 34 91 3
14Q LOSS WILD-TYPE 164 32 85 8

Figure S22.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'18p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000359 (Fisher's exact test), Q value = 0.21

Table S23.  Gene #71: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 245 66 176 11
18P LOSS MUTATED 31 9 46 5
18P LOSS WILD-TYPE 214 57 130 6

Figure S23.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'19p loss' versus 'Time to Death'

P value = 0.00017 (logrank test), Q value = 0.1

Table S24.  Gene #73: '19p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 497 166 0.1 - 120.6 (37.1)
19P LOSS MUTATED 11 9 1.4 - 109.9 (28.5)
19P LOSS WILD-TYPE 486 157 0.1 - 120.6 (37.2)

Figure S24.  Get High-res Image Gene #73: '19p loss' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = KIRC-TP.merged_data.txt

  • Number of patients = 498

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 9

  • Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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